Enhancing DNT Detection by a Bacterial Bioreporter: Directed Evolution of the Transcriptional Activator YhaJ

Development of lycopene-based whole-cell biosensors for the visual detection of trace explosives and heavy metals

Residual explosives in conflicting zones have caused irreversible damage to human safety and the environment. Whole-cell biosensors can to detect remnants of buried explosives, such as 2,4-dinitrotoluene (DNT), a stable and highly volatile compound in explosives. However, all the reported whole-cell biosensors utilize fluorescence or luminescence as the biological markers, making their detection difficult in real minefields. Here, we presented a lycopene-based whole-cell biosensor in Escherichia coli to output visible signals in response to DNT, which can help in the visual detection of buried explosives. To construct the whole-cell biosensor, the DNT-responsive promoter yqjF was used as the sensing element, and the lycopene synthetic gene cassette crtEBI was served as the reporting element. Then, the metabolic flux for lycopene production was enhanced to improve the output signal of the whole-cell biosensor, and a terminator was utilized to reduce the background interference. The optimized biosensor LSZ05 could perceive at least 1 mg/L DNT. The DNT-specificity and robust performance of the biosensor under different environmental factors were confirmed. Our results showed that converting the biosensor into a lyophilized powder was an effective storage method. The biosensor LSZ05 could effectively detect DNT in two kinds of soil samples. The lycopene-based whole-cell biosensor could also be used to visually detect heavy metals. Our findings laid the foundation for visually detecting buried explosives in minefields, which was a valuable supplement to the reported biosensors. The methods used for optimizing the lycopene-based whole-cell biosensor, including the improvement of the output signal and reduction of background interference, were quite effective.

Advancing biological investigations using portable sensors for detection of sensitive samples

Portable biosensors are emerged as powerful diagnostic tools for analyzing intricately complex biological samples. These biosensors offer sensitive detection capabilities by utilizing biomolecules such as proteins, nucleic acids, microbes or microbial products, antibodies, and enzymes. Their speed, accuracy, stability, specificity, and low cost make them indispensable in forensic investigations and criminal cases. Notably, portable biosensors have been developed to rapidly detect toxins, poisons, body fluids, and explosives; they have proven invaluable in forensic examinations of suspected samples, generating efficient results that enable effective and fair trials. One of the key advantages of portable biosensors is their ability to provide sensitive and non-destructive detection of forensic samples without requiring extensive sample preparation, thereby reducing the possibility of false results. This comprehensive review provides an overview of the current advancements in portable biosensors for the detection of sensitive materials, highlighting their significance in advancing investigations and enhancing sensitive sample detection capabilities.

Structural basis of transcription factor YhaJ for DNT detection

Detection of landmines without harming personnel is a global issue. The bacterial transcription factor YhaJ selectively detects metabolites of explosives, and it can be used as a key component of DNT biosensors. However, the wild-type YhaJ has a binding affinity that is not sufficient for the detection of trace amounts of explosives leaked from landmines buried in the soil. Here, we report crystal structures of the effector-binding domain of YhaJ in both the apo- and effector-bound forms. A structural comparison of the two forms revealed that the loop above the primary effector-binding site significantly switches its conformation upon effector binding. The primary effector-binding site involves hydrophobic and polar interactions, having specificity to hydroxyl-substituted benzene compounds. The structures explain the mechanism of activity-enhancing mutations and provide information for the rational engineering of YhaJ biosensors for the sensitive detection of explosives.

Controlling the sensitivity and selectivity for the detection of nitro-based explosives by modulating the electronic substituents on the ligand of AIPE-active cyclometalated iridium(III) complexes

Nitroaromatic compounds are extremely explosive materials that pose a national security risk and raise environmental concerns. The design and development of sensitive and selective compounds for explosive materials are highly desirable. 'Aggregation-Induced Emission' (AIE) active materials are best suited for sensing purposes because of their sensitivity, fast detection time, and easy operation. By rationally incorporating substituents on the cyclometalated (C^N) ligand, four different AIE active iridium(III) based monocyclometalated complexes with the general formula [Ir(PPh3)2(H)(Cl)(C^N)] were synthesized. The phenyl ring of the phenyl pyridine cyclometalated portion of an iridium(III) complex was substituted with the right substituents to adjust the FMO levels thus, leading to appropriate alignment of the energy levels. Each of the resulting complexes displayed a significant property known as 'Aggregation-Induced Phosphorescent Emission' (AIPE). The complexes were subjected to structural characterization, electrochemical analysis, and photophysical property studies. The synthesized complexes were employed for the detection of aromatic nitro explosive compounds such as trinitrophenol (TNP) and trinitrotoluene (TNT) in the aqueous phase with a high degree of sensitivity. The sensing capabilities of each complex were assessed for these nitro explosive compounds and compared to those of the unsubstituted iridium(III) complex (M). Notably, the best limits of detection for TNP and TNT have been achieved with iridium(III) complexes [M1 (489 pM) and M3 (3.6 nM)] within the literature reported until now. For detecting picric acid with M1, FRET was found to be the potential mechanism, and for TNT, PET was found to be the cause of emission quenching by M3. Furthermore, for low-cost detection, filter paper-based sensing was also found effective for each complex. Real-field sensing of PA in soil samples was also performed.

Performance upgrade of a microbial explosives' sensor strain by screening a high throughput saturation library of a transcriptional regulator

We present a methodology for a high-throughput screening (HTS) of transcription factor libraries, based on bacterial cells and GFP fluorescence. The method is demonstrated on the Escherichia coli LysR-type transcriptional regulator YhaJ, a key element in 2,4-dinitrotuluene (DNT) detection by bacterial explosives' sensor strains. Enhancing the performance characteristics of the YhaJ transcription factor is essential for future standoff detection of buried landmines. However, conventional directed evolution methods for modifying YhaJ are limited in scope, due to the vast sequence space and the absence of efficient screening methods to select optimal transcription factor mutants. To overcome this limitation, we have constructed a focused saturation library of ca. 6.4 × 107 yhaJ variants, and have screened over 70 % of its sequence space using fluorescence-activated cell sorting (FACS). Through this screening process, we have identified YhaJ mutants exhibiting superior fluorescence responses to DNT, which were then effectively transformed into a bioluminescence-based DNT detection system. The best modified DNT reporter strain demonstrated a 7-fold lower DNT detection threshold, a 45-fold increased signal intensity, and a 40 % shorter response time compared to the parental bioreporter. The FACS-based HTS approach presented here may hold a potential for future molecular enhancement of other sensing and catalytic bioreactions.

Design and optimization of E. coli artificial genetic circuits for detection of explosive composition 2,4-dinitrotoluene

The detection of mine-based explosives poses a serious threat to the lives of deminers, and carcinogenic residues may cause severe environmental pollution. Whole-cell biosensors that can detect on-site in dangerous or inaccessible environments have great potential to replace conventional methods. Synthetic biology based on engineering modularity serves as a new tool that could be used to engineer microbes to acquire desired functions through artificial design and precise regulation. In this study, we designed artificial genetic circuits in Escherichia coli MG1655 by reconstructing the transcription factor YhaJ-based system to detect explosive composition 2,4-dinitrotoluene (2,4-DNT). These genetic circuits were optimized at the transcriptional, translational, and post-translational levels. The binding affinity of the transcription factor YhaJ with inducer 2,4-DNT metabolites was enhanced via directed evolution, and several activator binding sites were inserted in sensing yqjF promoter (P_yqjF) to further improve the output level. The optimized biosensor P_yqjF×2-TEV-(mYhaJ + GFP)-Ssr had a maximum induction ratio of 189 with green fluorescent signal output, and it could perceive at least 1 μg/mL 2,4-DNT. Its effective and robust performance was verified in different water samples. Our results demonstrate the use of synthetic biology tools to systematically optimize the performance of sensors for 2,4-DNT detection, that lay the foundation for practical applications.

Introduction of quorum sensing elements into bacterial bioreporter circuits enhances explosives’ detection capabilities

A possible solution for the standoff detection of buried landmines is based on the use of microbial bioreporters, genetically engineered to emit a remotely detectable optical signal in response to trace amounts of explosives’ signature chemicals, mostly 2,4‐dinitrotoluene (DNT). Previously developed DNT sensor strains were based on the fusion of a DNT‐inducible gene promoter to a reporting element, either a fluorescent protein gene or a bacterial bioluminescence gene cassette. In the present study, a different approach was used: the DNT‐inducible promoter activates, in Escherichia coli, the quorum‐sensing luxI and luxR genes of Aliivibrio fischeri. N‐Acyl homoserine lactone (AHL), synthesized by LuxI, combines with LuxR and activates the bioluminescence reporter genes. The resulting bioreporter displayed a dose‐dependent luminescent signal in the presence of DNT. Performance of the sensor strain was further enhanced by manipulation of the sensing element (combining the E. coli DNT‐inducible azoR and yqjF gene promoters), by replacing the luminescence gene cassette of Photorhabdus luminescens luxCDABE with A. fischeri luxCDABEG, and by introducing two mutations, eutE and ygdD, into the host strain. DNT detection sensitivity of the final bioreporter was over 340‐fold higher than the original construct.